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Minor fixes for clang compilers
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x-chen committed Feb 1, 2018
1 parent 37bcaa6 commit cebfe2f
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Showing 6 changed files with 4 additions and 6 deletions.
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Expand Up @@ -21,7 +21,6 @@

#include "assembly/AssemblyReadInfo.hh"
#include "options/ReadScannerOptions.hh"
#include "options/SmallAssemblerOptions.hh"
#include "options/IterativeAssemblerOptions.hh"

typedef IterativeAssemblerOptions AssemblerOptions;
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2 changes: 1 addition & 1 deletion src/c++/lib/htsapi/bam_streamer.hh
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Expand Up @@ -66,7 +66,7 @@ struct bam_streamer : public stream_state_reporter, public boost::noncopyable
const char* referenceFilename,
const char* region = nullptr);

~bam_streamer();
~bam_streamer() override;

/// \brief Set new region to iterate over, this will fail if the alignment file is not indexed
///
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2 changes: 1 addition & 1 deletion src/c++/lib/manta/test/testUtil.hh
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Expand Up @@ -181,7 +181,7 @@ void addSupplementaryEvidence(
{
const char svtag[] = {'S','A'};
bam_aux_append(bamRead.get_data(),svtag,'Z',(svStr.size()+1),
(uint8_t*)(svStr.c_str()));
reinterpret_cast<uint8_t*>(const_cast<char*>(svStr.c_str())));
}

/// \brief Create the BamAlignment for a given read using the SimpleAlignment object.
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2 changes: 1 addition & 1 deletion src/c++/lib/options/IterativeAssemblerOptions.hh
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Expand Up @@ -24,7 +24,7 @@
///
struct IterativeAssemblerOptions
{
IterativeAssemblerOptions() = default;
IterativeAssemblerOptions() {}

/// the symbol set used during assembly
std::string alphabet = "ACGT";
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1 change: 0 additions & 1 deletion src/c++/lib/options/SVRefinerOptions.hh
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Expand Up @@ -21,7 +21,6 @@

#include "alignment/AlignmentScores.hh"
#include "options/IterativeAssemblerOptions.hh"
#include "options/SmallAssemblerOptions.hh"

typedef IterativeAssemblerOptions AssemblerOptions;

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2 changes: 1 addition & 1 deletion src/c++/lib/options/SmallAssemblerOptions.hh
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Expand Up @@ -24,7 +24,7 @@
///
struct SmallAssemblerOptions
{
SmallAssemblerOptions() = default;
SmallAssemblerOptions() {}

/// the symbol set used during assembly
std::string alphabet = "ACGT";
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